Talk:Genotype

The definition of genotype here is actually not common usage; quoting the "talking dictionary" used elsewhere on SNPedia http://www.genome.gov/glossary/index.cfm?id=93 : "A genotype is an individual's collection of genes. The term also can refer to the two alleles inherited for a particular gene." The terminology is generally extremely confusing, though. For example "allele" is defined to refer to whole gene, but common usage sees it frequently refer to a single nucleotide, in particular "minor allele frequency". See also http://dictionary.reference.com/browse/genotype ; official dictionaries do not allow for genotype to refer to a single SNP location. (But SNP itself is troublesome, because of the term "single nucleotide" can't be used to refer to both nucleotides at the locus, so some of this generally needs to be glossed over by necessity). Easiest solution is probably just to edit this page to say that genotype MAY refer to a collection of SNP's; in such a case it seems synymous with "genoset" though.

Yes, the usage is heavily context - and time - dependent, with the most common usage actually being a reference to the two alleles inherited for a particular gene ... and a single allele can wind being defined by a set of co-inherited SNPs and/or indels. But like other terms in genetics that have been in use for 100+ years, the usage is changing with time. And the difference between a genoset as a collection of SNPs and a genotype defined as you suggest is actually fairly significant, since genosets are commonly mixing SNPs from different chromosomes (and loci), whereas a genotype defined as two alleles is limited to a single locus (and obviously therefore a single chromosome).

Overall, though, it's a good idea to refer to the historic usage of the term genotype on this page, and indicate how it differs from the current usage, especially as used within SNPedia. I'll make an edit and if it doesn't go far enough or seems problematic feel free to comment and/or edit.Greg (talk) 20:07, 10 April 2014 (UTC)